Contacts of the helix formed by residues 412 - 422 (chain H) in PDB entry 1ZUM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 412 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311H GLN* 4.3 1.8 - - - +
410H PHE* 3.3 12.1 - - - -
411H LYS* 1.3 108.2 - - + +
413H ILE* 1.3 60.6 + - - +
414H GLU* 3.4 17.5 + - - +
415H GLU* 3.0 27.4 + - - +
416H VAL 3.0 23.2 + - - -
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Residues in contact with ILE 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278H MET* 3.9 22.9 - - + -
311H GLN* 4.5 3.8 - - - +
412H THR* 1.3 72.0 - - - +
414H GLU* 1.3 88.3 + - - +
416H VAL* 3.3 12.9 - - + +
417H VAL* 3.2 23.4 - - - +
438H LYS* 4.0 24.9 - - + -
441H TYR* 3.6 33.0 - - + -
442H LEU* 3.7 28.9 - - + -
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Residues in contact with GLU 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412H THR* 3.4 20.8 - - - +
413H ILE* 1.3 94.8 - - - +
415H GLU* 1.3 64.1 + - - +
417H VAL* 3.6 4.7 + - - +
418H GLY* 3.6 12.8 + - - -
441H TYR* 4.1 21.1 + - - +
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Residues in contact with GLU 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H PHE* 3.9 5.5 - - - -
411H LYS* 2.7 35.9 + - - +
412H THR* 3.0 22.7 + - - +
414H GLU* 1.3 74.2 - - - +
416H VAL* 1.3 65.6 + - - +
418H GLY* 3.1 12.8 + - - -
419H ARG* 2.9 51.7 + - + +
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Residues in contact with VAL 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ILE* 3.9 30.5 - - + -
309H PHE* 3.8 37.5 - - + -
410H PHE* 3.5 30.7 - - + -
412H THR 3.0 3.2 + - - +
413H ILE* 3.3 23.6 - - + +
415H GLU* 1.3 80.9 - - - +
417H VAL* 1.3 63.1 + - + +
419H ARG* 3.2 5.5 + - - +
420H ALA* 2.8 33.9 + - - +
442H LEU* 4.5 5.4 - - + -
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Residues in contact with VAL 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G LEU* 5.9 3.1 - - + -
413H ILE 3.2 15.9 + - - +
414H GLU* 3.7 9.0 - - - +
415H GLU 3.2 0.4 - - - -
416H VAL* 1.3 82.0 - - - +
418H GLY* 1.3 59.4 + - - +
420H ALA* 3.9 3.9 - - - +
421H ASN* 3.0 48.5 + - - +
441H TYR* 3.8 17.9 - - + +
442H LEU* 3.3 29.4 - - + -
445H ALA* 3.9 20.6 - - + +
446H LEU* 5.0 4.0 - - + -
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Residues in contact with GLY 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414H GLU 3.6 5.5 + - - -
415H GLU 3.1 7.3 + - - -
417H VAL* 1.3 83.3 - - - +
419H ARG* 1.3 55.4 + - - +
421H ASN* 3.8 4.3 - - - +
422H ASN* 3.0 31.1 + - - +
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Residues in contact with ARG 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ARG* 3.1 17.3 + - - -
309H PHE* 3.9 25.1 - - + -
389H VAL 4.7 3.4 + - - -
390H GLN* 5.2 4.9 - - - +
391H ASP* 2.9 47.5 + - - +
408H LEU* 3.9 12.1 - - - +
409H LYS 2.7 28.7 + - - -
410H PHE* 3.6 7.9 - - - +
415H GLU* 2.9 45.8 + - + +
416H VAL* 3.8 7.2 - - - +
418H GLY* 1.3 73.0 - - - +
420H ALA* 1.3 66.6 + - - +
422H ASN* 3.3 16.5 + - - +
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Residues in contact with ALA 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274H PRO* 3.7 32.6 - - + +
276H ILE* 4.1 7.2 - - + -
307H ARG* 3.0 25.2 + - - +
309H PHE* 4.3 6.4 - - + -
416H VAL 2.8 22.1 + - - +
417H VAL 3.9 0.2 - - - +
419H ARG* 1.3 71.8 - - - +
421H ASN* 1.3 61.8 + - - +
423H SER* 4.3 2.9 - - - -
446H LEU* 3.7 22.2 - - + -
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Residues in contact with ASN 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417H VAL* 3.0 33.6 + - - +
418H GLY* 4.0 5.1 - - - +
420H ALA* 1.3 75.1 - - - +
422H ASN* 1.3 53.7 + - - +
423H SER* 2.7 23.1 + - - +
445H ALA 3.0 23.4 + - - -
446H LEU* 3.5 9.0 - - - +
447H GLN* 2.8 56.6 + - + +
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Residues in contact with ASN 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ARG* 4.2 1.6 + - - -
391H ASP* 6.1 0.2 - - - +
418H GLY 3.0 18.2 + - - +
419H ARG* 3.7 13.2 - - - +
420H ALA 3.3 1.8 - - - -
421H ASN* 1.3 71.8 - - - +
423H SER* 1.3 66.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il